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1oge

From Proteopedia

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[[Image:1oge.gif|left|200px]]
 
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{{Structure
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==The Structure of Bacillus subtilis RbsD complexed with Ribose 5-phosphate==
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|PDB= 1oge |SIZE=350|CAPTION= <scene name='initialview01'>1oge</scene>, resolution 2.05&Aring;
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<StructureSection load='1oge' size='340' side='right'caption='[[1oge]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Rp5+Binding+Site+For+Chain+A'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=RP5:RIBOSE-5-PHOSPHATE, PYRANOSE FORM'>RP5</scene>
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<table><tr><td colspan='2'>[[1oge]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OGE FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oge OCA], [https://pdbe.org/1oge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oge RCSB], [https://www.ebi.ac.uk/pdbsum/1oge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oge ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RBSD_BACSU RBSD_BACSU] Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose (By similarity).[HAMAP-Rule:MF_01661]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/1oge_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oge ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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RbsD is the only protein whose biochemical function is unknown among the six gene products of the rbs operon involved in the active transport of ribose. FucU, a paralogue of RbsD conserved from bacteria to human, is also the only protein whose function is unknown among the seven gene products of the l-fucose regulon. Here we report the crystal structures of Bacillus subtilis RbsD, which reveals a novel decameric toroidal assembly of the protein. Nuclear magnetic resonance and other studies on RbsD reveal that the intersubunit cleft of the protein binds specific forms of d-ribose, but it does not have an enzyme activity toward the sugar. Likewise, FucU binds l-fucose but lacks an enzyme activity toward this sugar. We conclude that RbsD and FucU are cytoplasmic sugar-binding proteins, a novel class of proteins whose functional role may lie in helping influx of the sugar substrates.
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'''THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH RIBOSE 5-PHOSPHATE'''
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Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture.,Kim MS, Shin J, Lee W, Lee HS, Oh BH J Biol Chem. 2003 Jul 25;278(30):28173-80. Epub 2003 May 8. PMID:12738765<ref>PMID:12738765</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1oge" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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RbsD is the only protein whose biochemical function is unknown among the six gene products of the rbs operon involved in the active transport of ribose. FucU, a paralogue of RbsD conserved from bacteria to human, is also the only protein whose function is unknown among the seven gene products of the l-fucose regulon. Here we report the crystal structures of Bacillus subtilis RbsD, which reveals a novel decameric toroidal assembly of the protein. Nuclear magnetic resonance and other studies on RbsD reveal that the intersubunit cleft of the protein binds specific forms of d-ribose, but it does not have an enzyme activity toward the sugar. Likewise, FucU binds l-fucose but lacks an enzyme activity toward this sugar. We conclude that RbsD and FucU are cytoplasmic sugar-binding proteins, a novel class of proteins whose functional role may lie in helping influx of the sugar substrates.
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*[[Ribose-binding protein|Ribose-binding protein]]
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== References ==
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==About this Structure==
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<references/>
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1OGE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGE OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture., Kim MS, Shin J, Lee W, Lee HS, Oh BH, J Biol Chem. 2003 Jul 25;278(30):28173-80. Epub 2003 May 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12738765 12738765]
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[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Kim, M S.]]
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[[Category: Kim M-S]]
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[[Category: Oh, B H.]]
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[[Category: Oh B-H]]
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[[Category: CL]]
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[[Category: RP5]]
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[[Category: ribose 5-phosphate]]
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[[Category: sugar transport]]
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[[Category: transport]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:10:31 2008''
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Current revision

The Structure of Bacillus subtilis RbsD complexed with Ribose 5-phosphate

PDB ID 1oge

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